feature_annotation/align_query_reference

Description

Alignment of a query and reference dataset by:

Alignment of layers
Harmonization of .obs field names for batch and cell type labels
Harmonization of .var field name for gene names
Sanitation of gene names
Cross-checking of genes
Assignment of an id to the query and reference datasets

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
input_id: [ "query" ]  
reference_id: [ "reference" ]  
output_query: "$id.$key.output_query.h5mu"  
output_reference: "$id.$key.output_reference.h5mu"  
output_layer: [ "_counts" ]  
output_layer_lognormalized: [ "_log_normalized" ]  
output_var_gene_names: [ "_gene_names" ]  
output_obs_batch: [ "_sample_id" ]  
output_obs_label: [ "_cell_type" ]  
output_obs_id: [ "_dataset" ]  
output_var_index: [ "_ori_var_index" ]  
output_var_common_genes: [ "_common_vars" ]  
input_reference_gene_overlap: [ 100 ]  
align_layers_raw_counts: [ true ]  
unkown_celltype_label: [ "Unknown" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/feature_annotation/align_query_reference/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input (query) data to be labeled. Should be a .h5mu file.
--modality	string	Which modality to process. Note that the query and reference modalities should be the same.
--input_layer	string	The layer in the input (query) data containing raw counts if .X is not to be used.
--input_layer_lognormalized	string	The layer in the input (query) data containing log normalized counts if .X is not to be used.
--input_var_gene_names	string	The name of the .var column in the input (query) data containing gene names; when no gene_name_layer is provided, the var index will be used.
--input_obs_batch	string required	The name of the .obs column in the input (query) data containing batch information.
--input_obs_label	string	The name of the .obs column in the input (query) data containing cell type labels. If not provided, the --unkown_celltype_label will be assigned to all observations.
--input_id	string	Meta id value to be assigned to the --output_obs_id .obs field of the aligned input (query) data.

Name

Type & Properties

--input

file

required

--modality

string

--input_layer

string

--input_layer_lognormalized

string

--input_var_gene_names

string

--input_obs_batch

string

required

--input_obs_label

string

--input_id

string

Reference

Name	Type & Properties	Description
--reference	file	The reference data to train the CellTypist classifiers on. Only required if a pre-trained --model is not provided.
--reference_layer	string	The layer in the reference data containing raw counts if .X is not to be used. Data are expected to be processed in the same way as the --input query dataset.
--reference_layer_lognormalized	string	The layer in the reference data containing log normalized counts if .X is not to be used. Data are expected to be processed in the same way as the --input query dataset.
--reference_var_gene_names	string	The name of the .var column in the reference data containing gene names; when no gene_name_layer is provided, the var index will be used.
--reference_obs_batch	string required	The name of the .obs column in the reference data containing batch information.
--reference_obs_label	string	The name of the .obs column in the reference data containing cell type labels. If not provided, the --unkown_celltype_label will be assigned to all observations.
--reference_id	string	Meta id value to be assigned to the --output_obs_id .obs field of the aligned reference data.

Name

Type & Properties

--reference

file

--reference_layer

string

--reference_layer_lognormalized

string

--reference_var_gene_names

string

--reference_obs_batch

string

required

--reference_obs_label

string

--reference_id

string

Outputs

Name	Type & Properties	Description
--output_query	file output	Aligned query data.
--output_reference	file output	Aligned reference data.
--output_layer	string	Name of the aligned layer containing raw counts in the output query and reference datasets.
--output_layer_lognormalized	string	Name of the aligned layer containing log normalized counts in the output query and reference datasets.
--output_var_gene_names	string	Name of the .var column in the output query and reference datasets containing the gene names.
--output_obs_batch	string	Name of the .obs column in the output query and reference datasets containing the batch information.
--output_obs_label	string	Name of the .obs column in the output query and reference datasets containing the cell type labels.
--output_obs_id	string	Name of the .obs column in the output query and reference datasets containing the dataset id.
--output_var_index	string	Name of the .var column to which the .var index of the --input and --reference datasets is stored. Only relevant if "--preserve_var_index" is False.
--output_var_common_genes	string	Name of the .var column in the output query and reference datasets containing the boolean array indicating the common variables.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output_query

file

output

--output_reference

file

output

--output_layer

string

--output_layer_lognormalized

string

--output_var_gene_names

string

--output_obs_batch

string

--output_obs_label

string

--output_obs_id

string

--output_var_index

string

--output_var_common_genes

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--input_reference_gene_overlap	integer	The minimum number of genes present in both the reference and query datasets.
--align_layers_raw_counts	boolean	Whether to align the query and reference layers containing raw counts.
--align_layers_lognormalized_counts	boolean_true	Whether to align the query and reference layers containing log normalized counts.
--unkown_celltype_label	string	The label to assign to cells with an unknown cell type.
--overwrite_existing_key	boolean_true	If set to true and the layer, obs or var key already exists in the query/reference file, the key will be overwritten.
--preserve_var_index	boolean_true	If set to true, the .var index of the --input and --reference datasets will be preserved. If set to false (default behavior), the original .var index will be stored in the --output_var_index .var column and the .var index will be replaced with the sanitized & aligned gene names.

Name

Type & Properties

--input_reference_gene_overlap

integer

--align_layers_raw_counts

boolean

--align_layers_lognormalized_counts

boolean_true

--unkown_celltype_label

string

--overwrite_existing_key

boolean_true

--preserve_var_index

boolean_true